MicroRNA expression profiling and functional analysis in prostate cancer. Marco Folini s.c. Ricerca Traslazionale DOSL

Transcription

1 MicroRNA expression profiling and functional analysis in prostate cancer Marco Folini s.c. Ricerca Traslazionale DOSL

2 What are micrornas? For almost three decades, the alteration of protein-coding genes (PCGs) have been thought to be the cause of tumorigenesis With the discovery of genes that produce non-coding RNA (ncrna) transcripts, it became evident that the genomic complexity of cancer cells is far greater than expected Cancer is a complex genetic disease involving abnormal changes in Coding genes (PCGs) Non coding genes (e.g. microrna)

3 What are micrornas? A lesson from Caenhorabditis elegans First described in C. elegans: essential genes for the temporal control (small temporal RNAs) of diverse developmental events: Lin-4 acts by negatively regulating the level of LIN-14 protein via an antisense RNA-RNA interaction. Lee RC, Feinbaum RL, Ambros V. The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 1993;75(5): let-7 encodes a temporally regulated 21-nucleotide RNA that is complementary to elements in the 3' untranslated regions of the heterochronic genes lin-14, lin-28, lin-41, lin-42 and daf-12. >3,000 mirnas have been identified in the last 5 years in viruses, worms, flies, plants and vertebrates

4 What are micrornas? At a glance small non protein-coding regulatory RNAs (ncrnas) over 50% of human proteincoding genes regulated by mirnas post-transcriptional silencing: cleavage or inhibition of the translation of the target mrna

5 Role of mirnas MiRNAs are involved in essential biological processes development cell proliferation cell adhesion angiogenesis proteolysis and cell signalling apoptosis stem cell differentiation

6 mirnas and cancer First piece of evidence connecting mirnas and cancer mir-15 and mir-16 as target genes of the 13q14 deletion that is common in CLL (Calin et al. 2002) More than half of the known mirnas have been reported ->to be located in cancer-associated genomic regions ->to show copy number alterations in cancer ->to be deregulated in various cancers (mir-21, let-7 family) Some mirnas have been shown to negatively regulate oncogenes (mir- 15/BCL-2; let-7/ras) The mirna signatures of cancers of different cellular origin seem to be unique

7 Calin GA, Croce CM. Nature Reviews Cancer 6, 2006 Abnormal expression of mirnas has been detected in many types of human tumours, both solid and haematopoietic (breast cancer, lung cancer, colon cancer, thyroid papillary carcinoma, glioblastoma, B-CLL, BL ). Aberrant gene expression (abnormal levels of expression for mature and/or precursor mirna sequences) compared with the corresonding normal tissues microarrays bead-based flow cytometric mirna expression qrt-pcr

8 Causes of abnormal mirna expression Deletion Mutation Hypermethylation Abnormal mirna processing Amplification Translocation

9 mirnas as oncogenes and tumor suppressors MiRNAs have been proposed to contribute to oncogenesis because they can function either as tumor suppressors (as is the case for mir-15a and mir-16-1) or oncogenes (as is the case for mir-155 or members of the mir cluster). OG TS

10 mirnas as oncogenes and tumor suppressors

11 How to exploit mirnas? mirna expression profiles can lead to the identification of specific signatures that would allow: Diagnosis tumor vs. normal subtype of tumors SS RMS LMS NSM GIST Prognosis correlation with survival mir-155, let-7 in lung cancer association with proliferation index mir-21 & Ki67 endocrin pancreatic tumors Therapy direct targets (mir-21 in glioblastoma) identification of unknown targets

12 How to exploit mirnas for therapeutic purposes?

13 mirna and prostate cancer there is a limited number of studies on the role of mirnas in CaP

14 A microrna expression signature of human solid tumors defines cancer gene targets (Volinia S. et al. PNAS, 2006) Clustering analysis of 540 samples representing six solid cancers (363) and the respective normal tissues (177): 137 (out of 228) mirnas expressed in at least 90% of samples Initialcomparisonof alltumorsvs. allnormalsamples -> good separation between the different tissues -> solid cancer mirna signature: 43 out of 137 mirna deregulated (26 overexpressed and 17 underexpressed) mirna expression is heavily tissue specific -> identify mirna that are really prognostic for cancer status without incurring in the bias due to tissue specificity

15 Identification of the six tissue-specific signatures and then selection of mirnas shared among the different histotypes Prostate samples (63): 56 CaP and 7 normal tissues The predicted targets for differentially expressed mirnas are specifically enriched for proteincoding tumor suppressors and oncogenes

16 MicroRNA expression profiles classify human cancers (Lu et al. Nature 2005) 217 mirnas 129 out of 217 mirnas had lower expression levels in tumors compared with normal tissues Prostate samples (14): 6 CaP and 8 normal tissues

17 Unsupervised hierarchical clustering of prostate needle core biopsies (Mattie MD et al. Mol Cancer 2006) a core biopsy of an advanced prostatic tumor (Gleason score 8) a FNA of a prostatic lymph node metastasis PC3 and LNCaP prostate tumor cell lines (reference samples), a pooled normal adjacent to tumor sample a sample consisting of transitional cell metaplasia

18 480 mirnas Widespread deregulation of microrna expression in human prostate cancer (Ozen M. et al. Oncogene 2007) 10 benign peripheral zone 16 prostate cancer tissues 75 down-regulated mirnas

19 MicroRNA expression profiling in prostate cancer (Porkka K.P. et al. Cancer Res, 2007) 319 mirnas

20 MicroRNA expression profiling in prostate cancer (Porkka K.P. et al. Cancer Res, 2007) 51 differentially expressed mirnas

21 Microarray analysis ( data from our lab) (256 mirnas) Unsupervised hierarchical clustering Average phenotype scatterplot 5 3 cancer normal 46 differentially expressed mirnas 6 up-regulated & 40 down-regulated in tumor cell lines vs. normal sample Identification of a specific signature in androgen-refractory (DU145 and PC-3) vs. androgen-responsive (LNCaP) cancer cell lines -> 32 up-regulated and 12 down-regulated mirna